The win gives the Spanish two wins from their first two qualifying matches after Friday's 7-0 win in Belgium.
The reigning World Cup and UEFA Nations League champions had to work hard in the first half against the side ranked 30th in the world in a packed El Plantio Stadium in the historic northern city of Burgos, reports Xinhua.
The Czechs were solid in defense and Spain's early attacks were from winger Eva Navarro, who find space down the right flank.
Alexia Putellas and Lucia Garcia failed to capitalize on one ball into the area.
Garcia should have opened the scoring when Alexia put her through on goal, but her shot lacked conviction and Barbora Votikova was able to save.
Kamila Dubkova also shocked the World Champions at the other end when a deflected ball fell kindly for her, but her looping effort was just over the bar, before Alexia curled just wide, with some fans already celebrating a goal.
The Czechs took the lead after 55 minutes after good work from Klara Cahynova saw the ball roll to the edge of the area, where Aneta Pochmanova fired into the corner of the net.
The lead only lasted a minute before Maria Mendez headed Spain level from a corner and Jenni Hermoso put the home side ahead after being slipped through by Mariona Caldentey.
Caldentey added a third on 70 minutes after cutting inside and scoring with her right foot and what had looked as if it could turn into a difficult evening for the Spanish ended up being another comfortable win.
